RetrogeneDB ID: retro_sara_139

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_4304:88609..89413(-)
• Located in intron of: ENSSARG00000006776

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSSARG00000008477
• Aliases: None
• Description: male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]

Sequence

>retro_sara_139
GTGGACCTTTGTAAGGAGATGGTGGATGGGCTGAGGATAACCTTTGATCACATGCTCCCGCTGGTTCTGCTGTATCCGTA
TGAACAAGAGCAATATAAAATGGCGACGTCGTCCACAGGTTTTCTTCCGGTGAGGGACAGCGCCACCGACACGAACAGAA
GCTCAGAGGAGCTCTCTCCTAGCCCACCTTTAGAGAATCCGGCGGCCGCACAACCCACGGAGGGTCAGCCAGTGGCCGGG
GAGCCTACCACCCCCAAAAGGCGCAGAGCCGATCCGGAAGTTTTGCTGTCTCTGCGGCGCTCCACACGCCACTCAGTCAG
CTGTGACACCCTGTCGGAAAGAGGGGCCTCCCTGCAAGCCTTGCGCCAGCAGCAGGACACAGCCGCCGGCAGGCTGCCCT
TCCTGCACCTGGAAAAGACGACACCAGTGCAAAGCAGCTCCAGCTCATCTGTCCTTCTGACCCTGAATCATGAAGGGAGC
ATTGTGTTCGCTGGCGTGGAAGGCAGATCTCAAGAAATAAATGAAGTACTTGCCTGGAAACTTATGCCTGAAAGTTACCC
GCCCAGTGACCTGCCACCTCCAGCCTCTTGCATTTATGGGGCACAACATTTGCTGCGATTGTTTGTGAAACTTCCAGAAA
TCCTTGGAAAGATGTCCCTGCCTGAGAAGAACCTGAAGGCGTTGCTGAAGCACTTAGATCTCTTCCTGCAGTTTTTAGCA
GAATACCATGATGACTTCTTCCCTGAGTCAGCCTATGTGGCTGCCTGTGAGGCGCACAGTAGCACCAAACCCCCCAGGGC
TATG

Alignment

ORF - retro_sara_139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.19 %
• Parental protein coverage: 59.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLCKEMVDGLRITFDYTLPLVLLYPYEQVQYKKVTSSKFFLPIKESATNSNRNQEELSPSPPLLNPSTP
          VDLCKEMVDGLRITFD..LPLVLLYPYEQ.QYK..TSS..FLP...SAT..NR..EELSPSPPL.NP...
Retrocopy VDLCKEMVDGLRITFDHMLPLVLLYPYEQEQYKMATSSTGFLPVRDSATDTNRSSEELSPSPPLENPAAA

Parental  QSTESQPASGEPATPKRRKAEPEALQSLRRSTRHSASCDRLSESSASPQPKRRQQDTSANMPKLFLHLEK
          Q.TE.QP..GEP.TPKRR.A.PE.L.SLRRSTRHS.SCD.LSE..AS.Q..R.QQDT.A.....FLHLEK
Retrocopy QPTEGQPVAGEPTTPKRRRADPEVLLSLRRSTRHSVSCDTLSERGASLQALRQQQDTAAGRLP-FLHLEK

Parental  KTPVHSRSSSPVPLTPSKEGNTVLAGFEGRRTNEINEVLSWKLVPESYPPSDQPPPASFIYGAQHLLRLF
          .TPV.S.SSS.V.LT...EG..V.AG.EG.R..EINEVL.WKL.PESYPPSD.PPPAS.IYGAQHLLRLF
Retrocopy TTPVQSSSSSSVLLTLNHEGSIVFAGVEG-RSQEINEVLAWKLMPESYPPSDLPPPASCIYGAQHLLRLF

Parental  VKLPEILGKMSFAEKNLKALLKHFDLFLRFLAEYHDDFFPESAYVAACEAHYSTKNPRAI
          VKLPEILGKMS..EKNLKALLKH.DLFL.FLAEYHDDFFPESAYVAACEAH.STK.PRA.
Retrocopy VKLPEILGKMSLPEKNLKALLKHLDLFLQFLAEYHDDFFPESAYVAACEAHSSTKPPRAM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_139 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139 ,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,